Atomic heating on single atoms (SAs) to maximize the catalytic efficiency of each active site would be a fascinating solution to break the bottleneck for the performance improvement of single-atom catalysts (SACs) but highly challenging task. Here, based on the Gd@MoS2 SACs synthesized by a facile laser molecular beam epitaxy method, high-frequency alternating magnetic field (AMF) technology is employed to induce atomic magnetic heating on Gd SAs that is meanwhile demonstrated to be the catalytic active center. Significant improvement in catalytic kinetics under AMF excitation (3.9 mT) is achieved, yielding a remarkable enhancement of hydrogen evolution reaction magnetothermal-current by approximate to 924%. Through theoretical calculations and spin-related electrochemical experiments, such promotion in catalyst activity can be attributed to spin flip (or canting) in Gd SAs leading to the atomic magnetic heating effect on catalytic active center. Together with the embodied high stability, the implement of AMF to the SAs field is demonstrated in this work, and the precisely atomic magnetic heating on specific SAs offers unprecedented thinking for further improvement of SACs performance in the future.